Defining the healthy "core microbiome" of oral microbial communities

Abstract

BackgroundMost studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing).ResultsWe sampled and sequenced microbiomes from several intraoral niches (dental surfaces, cheek, hard palate, tongue and saliva) in three healthy individuals. Within an individual oral cavity, we found over 3600 unique sequences, over 500 different OTUs or "species-level" phylotypes (sequences that clustered at 3% genetic difference) and 88 - 104 higher taxa (genus or more inclusive taxon). The predominant taxa belonged to Firmicutes (genus Streptococcus, family Veillonellaceae, genus Granulicatella), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Corynebacterium, Rothia, Actinomyces), Bacteroidetes (genus Prevotella, Capnocytophaga, Porphyromonas) and Fusobacteria (genus Fusobacterium).Each individual sample harboured on average 266 "species-level" phylotypes (SD 67; range 123 - 326) with cheek samples being the least diverse and the dental samples from approximal surfaces showing the highest diversity. Principal component analysis discriminated the profiles of the samples originating from shedding surfaces (mucosa of tongue, cheek and palate) from the samples that were obtained from solid surfaces (teeth).There was a large overlap in the higher taxa, "species-level" phylotypes and unique sequences among the three microbiomes: 84% of the higher taxa, 75% of the OTUs and 65% of the unique sequences were present in at least two of the three microbiomes. The three individuals shared 1660 of 6315 unique sequences. These 1660 sequences (the "core microbiome") contributed 66% of the reads. The overlapping OTUs contributed to 94% of the reads, while nearly all reads (99.8%) belonged to the shared higher taxa.ConclusionsWe obtained the first insight into the diversity and uniqueness of individual oral microbiomes at a resolution of next-generation sequencing. We showed that a major proportion of bacterial sequences of unrelated healthy individuals is identical, supporting the concept of a core microbiome at health.

Saliva microbiomes distinguish caries-active from healthy human populations

“…For each sample, different reference databases gave similar relative proportions of the six major phyla (that is, Firmicutes, Proteobacteria, Actinobacteria, Fusobacteria, Bacteroidetes and Spirochaetes). Among different hosts, these six major phyla constituted the club of predominant oral residents, consistent with previous 16S rRNA gene-based community profiling surveys (Keijser et al, 2008;Zaura et al, 2009;Ling et al, 2010). However, the relative abundance of the predominant phyla differed among human hosts.…”

“…Among the 26 healthy and 19 caries-active hosts, only 0.53% and 0.08% species-level OTUs were shared, respectively. This finding contrasted with a recent report supporting the concept of a core microbiome, in which saliva microbiomes from three healthy Caucasian male adults shared 387 (47%) of 818 total OTUs (Zaura et al, 2009). The overly stringent read-selection criterion, as discussed above, could have led to this conclusion, where oral ecosystem could have been oversimplified by neglecting the 'rare phylotypes'.…”

“…Furthermore, the saliva microbial diversity in our study as measured by the number of OTUs in each sample was far greater than one recent estimate for three healthy Caucasian male adults (Zaura et al, 2009). One difference could be found in the readtrimming process: their analysis only focused on sequences occurring at least five times.…”

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

“…Earlier studies using cloning and Sanger sequencing (Kumar et al, 2005(Kumar et al, , 2006 suffered from the shallowness of the sequencing effort; it simply wasn't economically possible to obtain enough sequence information to plumb the complexity of the system. The advent of 454 pyrosequencing of 16S rRNA genes has allowed the collection of thousands of sequences per sample (Keijser et al, 2008;Zaura et al, 2009), and provides the power to comprehensively study bacterial community composition at the level of species. We used this technique to compare samples from patients with periodontitis and healthy controls, to further our understanding of bacterial ecology in this disease.…”

Speeksel en wondgenezing

“…Zo vormen de omstandigheden in de mond een ideale voedingsbodem voor het ontstaan van een zeer complexe microbiota, die meer dan 1.000 verschillende soorten bacteriën, schimmels en virussen omvat (Zaura et al, 2009). Het aantal bacteriën in de mond wordt geschat op 10 8 -10 9 .…”